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Abstract
StrAl is an alignment tool designed to provide multiple alignments of non-coding RNAs
following a fast progressive strategy. It combines the thermodynamic base pairing
information derived from RNAfold calculations in the form of base pairing probability vectors
with the information of the primary sequence. Thus the scoring system is composed of two major
parts evaluating the given structural and the sequence information, respectively. We apply an affine
gap weight model to our scoring system, which also allows for weighting the structure evaluation
against the sequence evaluation through the factor α. For an in-depth description of our
algorithm see the publication listed below.
Usage
The StrAl webservice can handle nearly all of the common alignment formats. If you wish to alter some
of the programs' parameters please use the advanced submission form.
Here you are able to choose from different guide tree methods and to adjust gap penalty values as well as the
structure weighting factor α. Currently the service is restricted to alignments consisting of 50 sequences maximum
with an average length of 500nt.
Example
Please avoid non-alphanumerical signs, e.g. dots(.) in the annotation line.
Project Team
Publications
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